Michael Hanke
46d995ea2b
- console lexer for anything that is a console session - some other specialized lexers when it makes sense - always with prompt, when in a console session, or for commands that are meant to be executed Closes #1013
44 lines
2 KiB
ReStructuredText
44 lines
2 KiB
ReStructuredText
.. runrecord:: /basics/_examples/DL-101-133-102
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:language: console
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:workdir: dl-101/DataLad-101/midterm_project
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$ cat .datalad/config
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This recorded the image's origin on Singularity-Hub, the location of the
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image in the dataset under ``.datalad/environments/<NAME>/image``, and it
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specifies the way in which the container should be used: The line
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.. code-block:: ini
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cmdexec = singularity exec {img} {cmd}
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can be read as: "If this container is used, take the ``cmd`` (what you wrap in a
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:dlcmd:`containers-run` command) and plug it into a
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:shcmd:`singularity exec` command. The mode of calling Singularity,
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namely ``exec``, means that the command will be executed inside of the container.
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You can configure this call format by modifying it in the config file, or calling :dlcmd:`containers-add` with the option ``--call-fmt <alternative format>``.
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This can be useful to, for example, automatically bind-mount the current working directory in the container.
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In the alternative call format, the placeholders ``{img}``, ``{cmd}``, and ``{img_dspath}`` (a relative path to the dataset containing the image) are available.
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In all other cases with variables that use curly brackets, you need to escape them with another curly bracket.
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Here is an example call format that bind-mounts the current working directory (and thus the dataset) automatically:
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.. code-block:: console
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$ datalad containers-add --call-fmt 'singularity exec -B {{pwd}} --cleanenv {img} {cmd}'
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Note that the image is saved under ``.datalad/environments`` and the
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configuration is done in ``.datalad/config`` -- as these files are version
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controlled and shared with together with a dataset, your software
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container and the information where it can be reobtained from are linked
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to your dataset.
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This is how the ``containers-add`` command is recorded in your history:
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.. runrecord:: /basics/_examples/DL-101-133-103
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:language: console
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:workdir: dl-101/DataLad-101/midterm_project
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:cast: 10_yoda
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:notes: The software container got added to your datasets history
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$ git log -n 1 -p
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